List of works - Patricia L. Clark

%MinMax: A versatile tool for calculating and comparing synonymous codon usage and its impact on protein folding

scientific article published in November 2017

A conserved stable core structure in the passenger domain beta-helix of autotransporter virulence proteins

scientific article

ATP-independent control of autotransporter virulence protein transport via the folding properties of the secreted protein

scientific article published on 29 December 2011

Adding Protease Digestion to the Membrane Protein Toolbox

scientific article published on 13 January 2011

An alternative outer membrane secretion mechanism for an autotransporter protein lacking a C-terminal stable core

scientific article published on 20 October 2013

Autotransporters: The Cellular Environment Reshapes a Folding Mechanism to Promote Protein Transport

scientific article published on April 2012

Cavity formation before stable hydrogen bonding in the folding of a β-clam protein

scientific article published on 01 November 1997

Characterization of the protrimer intermediate in the folding pathway of the interdigitated beta-helix tailspike protein

scientific article published in April 2002

Climbing to the peak of nascent-chain knowledge

scientific article published in November 2016

Commonly used FRET fluorophores promote collapse of an otherwise disordered protein

scientific article published on 16 April 2019

Commonly-used FRET fluorophores promote collapse of an otherwise disordered protein

Conformations of co-translational folding intermediates

scientific article

Cotranslational folding increases GFP folding yield

scientific article

Cotranslational folding promotes beta-helix formation and avoids aggregation in vivo

scientific article published on 22 July 2008

DegP Chaperone Suppresses Toxic Inner Membrane Translocation Intermediates.

scientific article

Distinct cysteine sulfhydryl environments detected by analysis of Raman S-hh markers of Cys-->Ser mutant proteins.

scientific article

Disulfide Bond-Mediated Passenger Domain Stalling as a Structural Probe of Autotransporter Outer Membrane Secretion In Vivo

scientific article published on 01 January 2011

Dynamics and Energy Contributions for Transport of Unfolded Pertactin through a Protein Nanopore

scientific article published on 24 August 2015

Expanding Anfinsen's principle: contributions of synonymous codon selection to rational protein design

scientific article

Extracellular protease digestion to evaluate membrane protein cell surface localization.

scientific article published on 19 November 2015

Folding and unfolding of a non-fluorescent mutant of green fluorescent protein

scientific article

Folding the proteome

scientific article published on 11 June 2013

GRAFENE: Graphlet-based alignment-free network approach integrates 3D structural and sequence (residue order) data to improve protein structural comparison.

scientific article published on 2 November 2017

Homogeneous stalled ribosome nascent chain complexes produced in vivo or in vitro.

scientific article

How to Build a Complex, Functional Propeller Protein, From Parts

scientific article

Increased incidence of rare codon clusters at 5' and 3' gene termini: implications for function

scientific article

Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water.

scientific article published in October 2017

Measuring cotranslational folding of nascent polypeptide chains on ribosomes

scientific article published on 13 November 2009

Molecular chaperones: providing a safe place to weather a midlife protein-folding crisis

scientific article published in July 2016

Monoclonal antibody epitope mapping describes tailspike beta-helix folding and aggregation intermediates

scientific article published on 14 April 2005

Multiple driving forces required for efficient secretion of autotransporter virulence proteins

scientific article

Non-fluorescent mutant of green fluorescent protein sheds light on the mechanism of chromophore formation

scientific article published on 20 April 2018

Of linkers and autochaperones: an unambiguous nomenclature to identify common and uncommon themes for autotransporter secretion

scientific article

Pertactin beta-helix folding mechanism suggests common themes for the secretion and folding of autotransporter proteins

scientific article

Probing the folding pathway of a beta-clam protein with single-tryptophan constructs.

scientific article published in January 1998

Properties of protein unfolded states suggest broad selection for expanded conformational ensembles

scientific article published on 02 September 2020

Protein folding in the cell, from atom to organism

Protein folding in the cell: reshaping the folding funnel

scientific article published on 01 October 2004

Quality over quantity: optimizing co-translational protein folding with non-'optimal' synonymous codons

scientific article published on 16 June 2016

Rare codons cluster

scientific article

Response to Comment on “Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water”

scientific article published in Science

Roles for Synonymous Codon Usage in Protein Biogenesis

scientific article

Slow formation of aggregation-resistant beta-sheet folding intermediates

scientific article published in March 2010

Structure-based prediction reveals capping motifs that inhibit β-helix aggregation

scientific article

Synonymous codon substitutions perturb cotranslational protein folding in vivo and impair cell fitness

scientific article published on 03 February 2020

Vectorial transport and folding of an autotransporter virulence protein during outer membrane secretion

scientific article published on 26 January 2009

Widespread position-specific conservation of synonymous rare codons within coding sequences.

scientific article

List of works by Patricia L. Clark

%MinMax: A versatile tool for calculating and comparing synonymous codon usage and its impact on protein folding

A conserved stable core structure in the passenger domain beta-helix of autotransporter virulence proteins

ATP-independent control of autotransporter virulence protein transport via the folding properties of the secreted protein

Adding Protease Digestion to the Membrane Protein Toolbox

An alternative outer membrane secretion mechanism for an autotransporter protein lacking a C-terminal stable core

Autotransporters: The Cellular Environment Reshapes a Folding Mechanism to Promote Protein Transport

Cavity formation before stable hydrogen bonding in the folding of a β-clam protein

Characterization of the protrimer intermediate in the folding pathway of the interdigitated beta-helix tailspike protein

Climbing to the peak of nascent-chain knowledge

Commonly used FRET fluorophores promote collapse of an otherwise disordered protein

Commonly-used FRET fluorophores promote collapse of an otherwise disordered protein

Conformations of co-translational folding intermediates

Cotranslational folding increases GFP folding yield

Cotranslational folding promotes beta-helix formation and avoids aggregation in vivo

DegP Chaperone Suppresses Toxic Inner Membrane Translocation Intermediates.

Distinct cysteine sulfhydryl environments detected by analysis of Raman S-hh markers of Cys-->Ser mutant proteins.

Disulfide Bond-Mediated Passenger Domain Stalling as a Structural Probe of Autotransporter Outer Membrane Secretion In Vivo

Dynamics and Energy Contributions for Transport of Unfolded Pertactin through a Protein Nanopore

Expanding Anfinsen's principle: contributions of synonymous codon selection to rational protein design

Extracellular protease digestion to evaluate membrane protein cell surface localization.

Folding and unfolding of a non-fluorescent mutant of green fluorescent protein

Folding the proteome

GRAFENE: Graphlet-based alignment-free network approach integrates 3D structural and sequence (residue order) data to improve protein structural comparison.

Homogeneous stalled ribosome nascent chain complexes produced in vivo or in vitro.

How to Build a Complex, Functional Propeller Protein, From Parts

Increased incidence of rare codon clusters at 5' and 3' gene termini: implications for function

Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water.

Measuring cotranslational folding of nascent polypeptide chains on ribosomes

Molecular chaperones: providing a safe place to weather a midlife protein-folding crisis

Monoclonal antibody epitope mapping describes tailspike beta-helix folding and aggregation intermediates

Multiple driving forces required for efficient secretion of autotransporter virulence proteins

Non-fluorescent mutant of green fluorescent protein sheds light on the mechanism of chromophore formation

Of linkers and autochaperones: an unambiguous nomenclature to identify common and uncommon themes for autotransporter secretion

Pertactin beta-helix folding mechanism suggests common themes for the secretion and folding of autotransporter proteins

Probing the folding pathway of a beta-clam protein with single-tryptophan constructs.

Properties of protein unfolded states suggest broad selection for expanded conformational ensembles

Protein folding in the cell, from atom to organism

Protein folding in the cell: reshaping the folding funnel

Quality over quantity: optimizing co-translational protein folding with non-'optimal' synonymous codons

Rare codons cluster

Response to Comment on “Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water”

Roles for Synonymous Codon Usage in Protein Biogenesis

Slow formation of aggregation-resistant beta-sheet folding intermediates

Structure-based prediction reveals capping motifs that inhibit β-helix aggregation

Synonymous codon substitutions perturb cotranslational protein folding in vivo and impair cell fitness

Vectorial transport and folding of an autotransporter virulence protein during outer membrane secretion

Widespread position-specific conservation of synonymous rare codons within coding sequences.